The San Francisco Chronicle has reported that at least twice in the 1990s, an MCA mosque hosted Ayman al-Zawahiri, who would later go on to become al Qaeda's No. 2, and helped raise money for him.

MCA was named in a May 1991 Muslim Brotherhood document -- titled "An Explanatory Memorandum on the General Strategic Goal for the Group in North America" -- as one of the Brotherhood’s 29 likeminded "organizations of our friends" that shared the common goal of destroying America and turning it into a Muslim nation. These "friends" were identified by the Brotherhood as groups that could help teach Muslims "that their work in America is a kind of grand Jihad in eliminating and destroying the Western civilization from within and 'sabotaging' its miserable house by their hands ... so that ... God's religion [Islam] is made victorious over all other religions."